Structural determinants for NF‐Y subunit organization and NF‐Y/DNA association in plants

Abstract

SUMMARYNF‐Y transcription factor comprises three subunits: NF‐YA, NF‐YB and NF‐YC. NF‐YB and NF‐YC dimerize through their histone fold domain (HFD), which can bind DNA in a non‐sequence‐specific fashion while serving as a scaffold for NF‐YA trimerization. Upon trimerization, NF‐YA specifically recognizes the CCAAT box sequence on promoters and enhancers. In plants, each NF‐Y subunit is encoded by several genes giving rise to hundreds of potential heterotrimeric combinations. In addition, plant NF‐YBs and NF‐YCs interact with other protein partners to recognize a plethora of genomic motifs, as the CCT protein family that binds CORE sites. The NF‐Y subunit organization and its DNA‐binding properties, together with the NF‐Y HFD capacity to adapt different protein modules, represent plant‐specific features that play a key role in development, growth and reproduction. Despite their relevance, these features are still poorly understood at the molecular level. Here, we present the structures of Arabidopsis and rice NF‐YB/NF‐YC dimers, and of an Arabidopsis NF‐Y trimer in complex with the FT CCAAT box, together with biochemical data on NF‐Y mutants. The dimeric structures identify the key residues for NF‐Y HFD stabilization. The NF‐Y/DNA structure and the mutation experiments shed light on HFD trimerization interface properties and the NF‐YA sequence appetite for the bases flanking the CCAAT motif. These data explain the logic of plant NF‐Y gene expansion: the trimerization adaptability and the flexible DNA‐binding rules serve the scopes of accommodating the large number of NF‐YAs, CCTs and possibly other NF‐Y HFD binding partners and a diverse audience of genomic motifs.

Identification and Comprehensive Analysis of the Nuclear Factor-Y Family Genes Reveal Their Multiple Roles in Response to Nutrient Deficiencies in Brassica napus

“…The results indicate that the numbers of NF-Y family members have increased in plants. Therefore, these NF-Y family genes may combine with each other to form tens of thousands of potential heterotrimers in plants [ 16 ]. The differentiation of the NF-Y family genes may lead to the diversity of their functions.…”

Abscisic Acid and Flowering Regulation: Many Targets, Different Places

“…Light is necessary to stabilize the CO protein, and numerous light-dependent molecular mechanisms involved in this process have been described [ 13 ]. CO protein plays a key role in the transcriptional activation of the florigens, forming a trimeric complex with NUCLEAR FACTOR-Y (NF-Y) B and C subunits at CONSTANS RESPONSIVE elements (CORE) located at the promoter of FT [ 17 , 18 ]. NF-Ys are highly conserved trimeric transcription factors (TFs) formed by NF-YA, NF-YB, and NF-YC subunits involved in many developmental processes including flowering [ 19 ].…”

LSD3 mediates the oxidative stress response through fine‐tuning APX2 activity and the NF‐YC15‐GSTs module in cassava

“…Therefore, MeNF‐YC15 was also selected for further analysis. Considering NF‐YA, NF‐YB and NF‐YC usually form NF‐YA–NF‐YB–NF‐YC complexed to activate plant defense responses (Chaves‐Sanjuan et al., 2021; He et al., 2019), the interactions between MeNF‐YC15, MeNF‐YAs and MeNF‐YBs were investigated by point‐to‐point yeast two‐hybrid assay. The results showed that MeNF‐YA2/YA4 and MeNF‐YB18 interacted with MeNF‐YC15 (Figure 4a).…”

“…Considering the essential role of MeLSD3 in oxidative stress responses, MeGST‐U37 and MeGST‐U39 were selected for further analysis. Promoter region analysis revealed that CCAAT motifs, the targets of plant NF‐Y transcription factors (Chaves‐Sanjuan et al., 2021; He et al., 2019), were enriched in the promoters of MeGST‐U37 and MeGST‐U39 . We then tested whether they are direct targets of MeNF‐YC15.…”